U1A protein

U1A protein is an RNA-binding protein component of U1 snRNP. Its N-terminal RNA recognition motif binds stem-loopII of U1 small nuclear RNA, helping distinguish a specific RNA-binding interaction from the assembly of the entire small nuclear ribonucleoprotein.^[ref]

A1994 X-ray crystallography study determined a complex of the U1A RNA-binding domain and an RNA hairpin at $1.92\mathring{\mathrm{A}}$ resolution. This was a domain–RNA complex, not a structure of a complete spliceosome.^[ref]

For an original one-site binding example, suppose a domain binds one RNA molecule with dissociation constant $K_d$ and free RNA concentration $[R]$. Under the stipulated equilibrium model, the bound fraction of domains isIf $K_d=10\mathrm{nM}$, then $[R]=10\mathrm{nM}$ gives $f=1/2$, whereas $[R]=90\mathrm{nM}$ gives $f=0.9$. These invented constants illustrate binding affinity; they are not measured U1A values and assume free, rather than total, RNA concentration.

Binding of an isolated domain does not by itself demonstrate functional RNA splicing. A later U1-core crystallographic study omitted U1A from its engineered particle and added a previously known U1A–RNA structure when modeling the complete assembly. Distinguishing observed components from modeled additions is essential to interpreting that experiment.^[ref]